Here are a few notes on various bits of MCX stuff I'm gleaning as I go.
It seems that search domains are specified per interface and the interface key changes on each machine. At the moment I've decided to handle this in the system image as too hard under MCX.
The server used for Software Update is saved in /Library/Preferences/com.apple.SoftwareUpdate
The key has to be added to the file as “CatalogURL” and should be set to “http://server.domain.com:8088/”